It can be confusing but it's mainly for historical reasons.
At first there was only TouchPod (The classic M3Real).
The M3 Real was more expensive than other carts (like CycloDS), so they decided to release a new cart with a new loader (~ firmware) called iTouchDS that was cheaper and had less fonctionnality (like GBA playing).
Then the M3 Team decided to release a new cart (M3Sakura) which was in fact the same cart as the M3 Real but with a different loader (Sakura 'GUI').
The M3 Sakura GUI has a lot of bult-in multimedia functions, it was co-developped by the author of Moonshell which is an excellent multimedia homebrew player.
All these carts and loader are officially developped by the M3 Team (there is one sub-team in China and another in Japan if I'm right).
To sum up, there are 2 carts : M3 Real and iTouchDS, and there are 3 loaders, TouchPod and Sakura for M3 Real, and the iTouchDS loader.
Officially TouchPod and Sakura shouldn't work on iTouchDS and iTouchDS loader shouldn't work on M3 Real, but some guys have done it many times before (sometimes with hacking the loaders) ...
The difference between all them is that iTouchDS is said to be better for homebrew compatibility, TouchPod better for commercial game compatibility, and sakura has an owesome GUI with builtin multimedia playing but has a game compat. that is sometimes lower (need some cheat hacks with last games) and homebrew compat. is also lower than the two other.
In my opinion, when homebrew compat will be as good on sakura than on touchpod, touchpod could be left behind, because sakura is way better in terms of gui and multimedia playing.
I hope you understand better now.